Concurrent coupling of atomistic simulation and mesoscopic hydrodynamics for flows over soft multi-functional surfaces

Wang, Yuying; Li, Zhen; Xu, Junbo; Yang, Chao; Karniadakis, George Em

doi:10.1039/c8sm02170h

Concurrent coupling of atomistic simulation and mesoscopic hydrodynamics for flows over soft multi-functional surfaces

Journal Article · Mon Jan 14 23:00:00 EST 2019 · Soft Matter

DOI:https://doi.org/10.1039/c8sm02170h· OSTI ID:1613243

Wang, Yuying ^[1]; ^[2]; ^[3]; ^[4]; Karniadakis, George Em ^[2]

Chinese Academy of Sciences (CAS), Beijing (China); Brown Univ., Providence, RI (United States); University of Chinese Academy of Sciences, Beijing (China); DOE/OSTI
Brown Univ., Providence, RI (United States)
Chinese Academy of Sciences (CAS), Beijing (China)
Chinese Academy of Sciences (CAS), Beijing (China); University of Chinese Academy of Sciences, Beijing (China)

Here, we develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometers to microns and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an all-atom molecular dynamics (MD) description for specific atomistic details in the vicinity of the functional surface with a dissipative particle dynamics (DPD) approach that captures mesoscopic hydrodynamics in the domain away from the functional surface. In order to achieve a seamless transition in dynamic properties we endow the MD simulation with a DPD thermostat, which is validated against experimental results by modeling water at different temperatures. We then validate the MD-DPD coupling method for transient Couette and Poiseuille flows, demonstrating that the concurrent MD-DPD coupling can resolve accurately the continuum-based analytical solutions. Subsequently, we simulate shear flows over grafted polydimethylsiloxane (PDMS) surfaces (polymer brushes) for various grafting densities, and investigate the slip flow as a function of the shear stress. We verify that a “universal” power law exists for the slip length, in agreement with published results. Having validated the MD-DPD coupling method, we simulate time-dependent flows past an endothelial glycocalyx layer (EGL) in a microchannel. Coupled simulation results elucidate the dynamics of the EGL changing from an equilibrium state to a compressed state under shear by aligning the molecular structures along the shear direction. MD-DPD simulation results agree well with results of a single MD simulation, but with the former more than two orders of magnitude faster than the latter for system sizes above one micron.

View Accepted Manuscript (DOE)

Research Organization:: Brown Univ., Providence, RI (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Natural Science Foundation of China (NSFC); National Institutes of Health (NIH); US Army Research Office (ARO); Chinese Scholarship Council (CSC)

Grant/Contract Number:: SC0019453

OSTI ID:: 1613243

Alternate ID(s):: OSTI ID: 1710202
OSTI ID: 1491909

Journal Information:: Soft Matter, Journal Name: Soft Matter Journal Issue: 8 Vol. 15; ISSN 1744-683X

Publisher:: Royal Society of ChemistryCopyright Statement

Country of Publication:: United States

Language:: English

References (59)

Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
A calculation of the viscous force exerted by a flowing fluid on a dense swarm of particles Brinkman, H. C. Flow, Turbulence and Combustion, Vol. 1, Issue 1 https://doi.org/10.1007/BF02120313	journal	December 1949
The endothelial glycocalyx: composition, functions, and visualization Reitsma, Sietze; Slaaf, Dick W.; Vink, Hans Pflügers Archiv - European Journal of Physiology, Vol. 454, Issue 3 https://doi.org/10.1007/s00424-007-0212-8	journal	January 2007
The endothelial surface layer Pries, A. R.; Secomb, T. W.; Gaehtgens, P. Pflügers Archiv - European Journal of Physiology, Vol. 440, Issue 5 https://doi.org/10.1007/s004240000307	journal	April 2000
Oligosaccharide model of the vascular endothelial glycocalyx in physiological flow Pikoula, Maria; Tessier, Matthew B.; Woods, Robert J. Microfluidics and Nanofluidics, Vol. 22, Issue 2 https://doi.org/10.1007/s10404-018-2037-5	journal	January 2018
A Role for the Endothelial Glycocalyx in Regulating Microvascular Permeability in Diabetes Mellitus Perrin, Rachel M.; Harper, Steven J.; Bates, David O. Cell Biochemistry and Biophysics, Vol. 49, Issue 2 https://doi.org/10.1007/s12013-007-0041-6	journal	August 2007
VMD: Visual molecular dynamics Humphrey, William; Dalke, Andrew; Schulten, Klaus Journal of Molecular Graphics, Vol. 14, Issue 1 https://doi.org/10.1016/0263-7855(96)00018-5	journal	February 1996
Shear-induced permeability changes in a polymer grafted silica membrane Castro, Robert P.; Monbouquette, Harold G.; Cohen, Yoram Journal of Membrane Science, Vol. 179, Issue 1-2 https://doi.org/10.1016/S0376-7388(00)00509-3	journal	November 2000
Liposomal drug delivery systems: From concept to clinical applications Allen, Theresa M.; Cullis, Pieter R. Advanced Drug Delivery Reviews, Vol. 65, Issue 1 https://doi.org/10.1016/j.addr.2012.09.037	journal	January 2013
Structure and Response to Flow of the Glycocalyx Layer Cruz-Chu, Eduardo R.; Malafeev, Alexander; Pajarskas, Tautrimas Biophysical Journal, Vol. 106, Issue 1 https://doi.org/10.1016/j.bpj.2013.09.060	journal	January 2014
Large-scale molecular dynamics simulation of flow under complex structure of endothelial glycocalyx Jiang, Xi Zhuo; Feng, Muye; Luo, Kai H. Computers & Fluids, Vol. 173 https://doi.org/10.1016/j.compfluid.2018.03.014	journal	September 2018
Thermal conductivity, shear viscosity and specific heat of rigid water models Mao, Yijin; Zhang, Yuwen Chemical Physics Letters, Vol. 542 https://doi.org/10.1016/j.cplett.2012.05.044	journal	July 2012
Hybrid atomistic–continuum method for the simulation of dense fluid flows Werder, Thomas; Walther, Jens H.; Koumoutsakos, Petros Journal of Computational Physics, Vol. 205, Issue 1 https://doi.org/10.1016/j.jcp.2004.11.019	journal	May 2005
Triple-decker: Interfacing atomistic–mesoscopic–continuum flow regimes Fedosov, Dmitry A.; Karniadakis, George Em Journal of Computational Physics, Vol. 228, Issue 4 https://doi.org/10.1016/j.jcp.2008.10.024	journal	March 2009
Energy-conserving dissipative particle dynamics with temperature-dependent properties Li, Zhen; Tang, Yu-Hang; Lei, Huan Journal of Computational Physics, Vol. 265 https://doi.org/10.1016/j.jcp.2014.02.003	journal	May 2014
Multi-resolution flow simulations by smoothed particle hydrodynamics via domain decomposition Bian, Xin; Li, Zhen; Karniadakis, George Em Journal of Computational Physics, Vol. 297 https://doi.org/10.1016/j.jcp.2015.04.044	journal	September 2015
Multiscale Universal Interface: A concurrent framework for coupling heterogeneous solvers Tang, Yu-Hang; Kudo, Shuhei; Bian, Xin Journal of Computational Physics, Vol. 297 https://doi.org/10.1016/j.jcp.2015.05.004	journal	September 2015
A dissipative particle dynamics method for arbitrarily complex geometries Li, Zhen; Bian, Xin; Tang, Yu-Hang Journal of Computational Physics, Vol. 355 https://doi.org/10.1016/j.jcp.2017.11.014	journal	February 2018
Active learning of constitutive relation from mesoscopic dynamics for macroscopic modeling of non-Newtonian flows Zhao, Lifei; Li, Zhen; Caswell, Bruce Journal of Computational Physics, Vol. 363 https://doi.org/10.1016/j.jcp.2018.02.039	journal	June 2018
Formation of more stable hydrophilic surfaces of PDMS by plasma and chemical treatments Bodas, Dhananjay; Khan-Malek, Chantal Microelectronic Engineering, Vol. 83, Issue 4-9 https://doi.org/10.1016/j.mee.2006.01.195	journal	April 2006
Development of a PDMS-grafted alumina membrane and its evaluation as solvent resistant nanofiltration membrane Pinheiro, Ana F. M.; Hoogendoorn, Danny; Nijmeijer, Arian Journal of Membrane Science, Vol. 463 https://doi.org/10.1016/j.memsci.2014.03.050	journal	August 2014
PDMS grafting of mesoporous γ-alumina membranes for nanofiltration of organic solvents Tanardi, Cheryl R.; Pinheiro, Ana F. M.; Nijmeijer, Arian Journal of Membrane Science, Vol. 469 https://doi.org/10.1016/j.memsci.2014.07.010	journal	November 2014
Solvent permeation behavior of PDMS grafted γ-alumina membranes Tanardi, Cheryl R.; Vankelecom, Ivo F. J.; Pinheiro, Ana F. M. Journal of Membrane Science, Vol. 495 https://doi.org/10.1016/j.memsci.2015.08.004	journal	December 2015
Effect of grafting on microstructure, composition and surface and transport properties of ceramic membranes for osmotic evaporation Vargas-Garcia, A.; Torrestiana-Sanchez, B.; Garcia-Borquez, A. Separation and Purification Technology, Vol. 80, Issue 3 https://doi.org/10.1016/j.seppur.2011.05.030	journal	August 2011
A continuum and molecular dynamics hybrid method for micro- and nano-fluid flow Nie, X. B.; Chen, S. Y.; E., W. N. Journal of Fluid Mechanics, Vol. 500 https://doi.org/10.1017/S0022112003007225	journal	January 1999
Simulation and modelling of slip flow over surfaces grafted with polymer brushes and glycocalyx fibres Deng, Mingge; Li, Xuejin; Liang, Haojun Journal of Fluid Mechanics, Vol. 711 https://doi.org/10.1017/jfm.2012.387	journal	September 2012
50th Anniversary Perspective : Polymer Brushes: Novel Surfaces for Future Materials Chen, Wei-Liang; Cordero, Roselynn; Tran, Hai Macromolecules, Vol. 50, Issue 11 https://doi.org/10.1021/acs.macromol.7b00450	journal	May 2017
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins ^† MacKerell, A. D.; Bashford, D.; Bellott, M. The Journal of Physical Chemistry B, Vol. 102, Issue 18 https://doi.org/10.1021/jp973084f	journal	April 1998
Theory of the grafted polymer brush Milner, S. T.; Witten, T. A.; Cates, M. E. Macromolecules, Vol. 21, Issue 8 https://doi.org/10.1021/ma00186a051	journal	August 1988
Atomistic Simulation of Poly(dimethylsiloxane): Force Field Development, Structure, and Thermodynamic Properties of Polymer Melt and Solubility of n -Alkanes, n -Perfluoroalkanes, and Noble and Light Gases Μakrodimitri, Zoi Α.; Dohrn, Ralf; Economou, Ioannis G. Macromolecules, Vol. 40, Issue 5 https://doi.org/10.1021/ma062453f	journal	March 2007
Nonlinear Response of Grafted Semiflexible Polymers in Shear Flow Kim, Yong Woon; Lobaskin, V.; Gutsche, C. Macromolecules, Vol. 42, Issue 10 https://doi.org/10.1021/ma900184e	journal	May 2009
Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostat Junghans, Christoph; Praprotnik, Matej; Kremer, Kurt Soft Matter, Vol. 4, Issue 1 https://doi.org/10.1039/B713568H	journal	January 2008
Construction of dissipative particle dynamics models for complex fluids via the Mori–Zwanzig formulation Li, Zhen; Bian, Xin; Caswell, Bruce Soft Matter, Vol. 10, Issue 43 https://doi.org/10.1039/C4SM01387E	journal	January 2014
Brushes of semiflexible polymers in equilibrium and under flow in a super-hydrophobic regime Speyer, K.; Pastorino, C. Soft Matter, Vol. 11, Issue 27 https://doi.org/10.1039/C5SM01075F	journal	January 2015
Predicting the morphology of sickle red blood cells using coarse-grained models of intracellular aligned hemoglobin polymers Lei, Huan; Karniadakis, George Em Soft Matter, Vol. 8, Issue 16 https://doi.org/10.1039/c2sm07294g	journal	January 2012
The shear viscosity of rigid water models González, Miguel Angel; Abascal, José L. F. The Journal of Chemical Physics, Vol. 132, Issue 9 https://doi.org/10.1063/1.3330544	journal	March 2010
Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation Groot, Robert D.; Warren, Patrick B. The Journal of Chemical Physics, Vol. 107, Issue 11 https://doi.org/10.1063/1.474784	journal	September 1997
Tethered chains in poor solvent conditions: An experimental study involving Langmuir diblock copolymer monolayers Kent, M. S.; Majewski, J.; Smith, G. S. The Journal of Chemical Physics, Vol. 110, Issue 7 https://doi.org/10.1063/1.478223	journal	February 1999
Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems Li, Zhen; Yazdani, Alireza; Tartakovsky, Alexandre The Journal of Chemical Physics, Vol. 143, Issue 1 https://doi.org/10.1063/1.4923254	journal	July 2015
Perspective: Dissipative particle dynamics Español, Pep; Warren, Patrick B. The Journal of Chemical Physics, Vol. 146, Issue 15 https://doi.org/10.1063/1.4979514	journal	April 2017
Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics Zavadlav, Julija; Praprotnik, Matej The Journal of Chemical Physics, Vol. 147, Issue 11 https://doi.org/10.1063/1.4986916	journal	September 2017
Mechanotransduction and flow across the endothelial glycocalyx Weinbaum, S.; Zhang, X.; Han, Y. Proceedings of the National Academy of Sciences, Vol. 100, Issue 13 https://doi.org/10.1073/pnas.1332808100	journal	June 2003
The shear viscosities of common water models by non-equilibrium molecular dynamics simulations Song, Yanmei; Dai, Lenore L. Molecular Simulation, Vol. 36, Issue 7-8 https://doi.org/10.1080/08927021003720553	journal	June 2010
Surface graft polymerization of SU-8 for bio-MEMS applications Wang, Yuli; Pai, Jeng-Hao; Lai, Hsuan-Hong Journal of Micromechanics and Microengineering, Vol. 17, Issue 7 https://doi.org/10.1088/0960-1317/17/7/020	journal	June 2007
Static and dynamic properties of dissipative particle dynamics Marsh, C. A.; Backx, G.; Ernst, M. H. Physical Review E, Vol. 56, Issue 2 https://doi.org/10.1103/PhysRevE.56.1676	journal	August 1997
Counterion condensation and fluctuation-induced attraction Lau, A. W. C.; Pincus, P. Physical Review E, Vol. 66, Issue 4 https://doi.org/10.1103/PhysRevE.66.041501	journal	October 2002
Coupling lattice Boltzmann and molecular dynamics models for dense fluids Dupuis, A.; Kotsalis, E. M.; Koumoutsakos, P. Physical Review E, Vol. 75, Issue 4 https://doi.org/10.1103/PhysRevE.75.046704	journal	April 2007
Fluctuating hydrodynamics in periodic domains and heterogeneous adjacent multidomains: Thermal equilibrium Bian, Xin; Li, Zhen; Deng, Mingge Physical Review E, Vol. 92, Issue 5 https://doi.org/10.1103/PhysRevE.92.053302	journal	November 2015
The endothelial glycocalyx: a review of the vascular barrier Alphonsus, C. S.; Rodseth, R. N. Anaesthesia, Vol. 69, Issue 7 https://doi.org/10.1111/anae.12661	journal	April 2014
Blood Flow and Cell-Free Layer in Microvessels: Blood Flow and Cell-Free Layer in Microvessels Fedosov, Dmitry A.; Caswell, Bruce; Popel, Aleksander S. Microcirculation, Vol. 17, Issue 8 https://doi.org/10.1111/j.1549-8719.2010.00056.x	journal	November 2010
An Optimization-based Atomistic-to-Continuum Coupling Method Olson, Derek; Bochev, Pavel B.; Luskin, Mitchell SIAM Journal on Numerical Analysis, Vol. 52, Issue 4 https://doi.org/10.1137/13091734X	journal	January 2014
Nanoparticle Delivery of Cancer Drugs Wang, Andrew Z.; Langer, Robert; Farokhzad, Omid C. Annual Review of Medicine, Vol. 63, Issue 1 https://doi.org/10.1146/annurev-med-040210-162544	journal	February 2012
The Structure and Function of the Endothelial Glycocalyx Layer Weinbaum, Sheldon; Tarbell, John M.; Damiano, Edward R. Annual Review of Biomedical Engineering, Vol. 9, Issue 1 https://doi.org/10.1146/annurev.bioeng.9.060906.151959	journal	August 2007
Resistance to blood flow in microvessels in vivo. Pries, A. R.; Secomb, T. W.; Gessner, T. Circulation Research, Vol. 75, Issue 5 https://doi.org/10.1161/01.RES.75.5.904	journal	November 1994
Stretching of Grafted Polymer Layers Rabin, Y.; Alexander, S. Europhysics Letters (EPL), Vol. 13, Issue 1 https://doi.org/10.1209/0295-5075/13/1/009	journal	September 1990
Drug delivery and nanoparticles: Applications and hazards No authors listed International Journal of Nanomedicine https://doi.org/10.2147/IJN.S596	journal	June 2008
Perspective: Dissipative Particle Dynamics Español, Pep; Warren, Patrick B. arXiv https://doi.org/10.48550/arxiv.1612.04574	text	January 2016
A dissipative particle dynamics method for arbitrarily complex geometries Li, Zhen; Bian, Xin; Tang, Yu-Hang arXiv https://doi.org/10.48550/arxiv.1612.08761	text	January 2016
Counterion Condensation and Fluctuation-Induced Attraction Lau, A. W. C.; Pincus, P. arXiv https://doi.org/10.48550/arxiv.cond-mat/0209659	text	January 2002

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